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Which client are you using? It's usually better to post in the dedicated forum for that client.

When you say missing, where are they missing from? From the tag list? From notes that you've assigned them to?

In case it's Windows, I'll take a wild guess. Do you have the "Hide unassigned tags" set on your tag list? Right click on the "Tags" label at the root of the list, and if "Show unassigned tags" appears at the bottom of the menu; if that's the case, all tags that are not assigned to any of the current list of notes (as filtered by the search criteria) will not appear in the tag list, which might cause what you are seeing. Click that option, and the tags should appear.

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I just experienced the same problem - Windows client. And "Hide unassigned tags" is not set. Evernote is letting the core functionality slip while dithering with Skitch and all the other ***** they're working on.